2. Natural Products in Drug Discovery & Development (copy)

Major Historical vs. Current Role of Natural Products

Historically, nature/plants were important origins of drugs of choice. Currently, synthetic drugs are the major use, but natural products remain important sources of drug leads and structural backbones.

Unmodified Natural Product Share (1981–2006)

6%

Modified Natural Product Share (1981–2006)

28%

Synthetic Product Share (1981–2006)

37%

Synthetic Product w/ Natural Product Pharmacophore Share (1981–2006)

5%

Synthetic Product w/ Natural Product Pharmacophore & Competitive Inhibitor Share (1981–2006)

12%

Synthetic Product Competitive Inhibitor of Natural Substrate Share (1981–2006)

12%

Digoxin Source

Digitalis purpurea

Digoxin Drug Class & Mechanism of Action

Cardiac glycoside that inhibits sodium-potassium pumps (Na+/K+-ATPase)

Quinine Source

Cinchona officinalis

Quinine Pharmacological Indication

Antimalarial

Vincristine & Vinblastine Source

Catharanthus roseus

Vincristine & Vinblastine Mechanism of Action & Indication

Anticancer drugs that stabilize microtubules and inhibit cell growth by disrupting mitosis

Reserpine Source

Rauwolfia serpentina

Reserpine Indication

Treatment for hypertension and CNS depressant

Main Sustainability Solution for Natural Products

Convention on Biological Diversity

Convention on Biological Diversity Objectives

Conservation and sustainable use of biological diversity, fair/equitable sharing of benefits from genetic resources, and prevention of overexploitation and possible extinction

CBD Certification Hierarchy

Proceeds from LGU → Municipality → Higher levels

Genetic Diversity Definition

Variations of genes within a species (e.g., Genome-wide SNP and InDel analysis in mango)

Single-Nucleotide Polymorphism (SNP)

Variations of a genetic sequence by one nucleotide base.

Transition

Transition is a purine-to-purine or pyrimidine-to-pyrimidine base change

Transversion

Transversion is a purine-to-pyrimidine or pyrimidine-to-purine base chang

Species Diversity Definition

A variety of different species found in a particular area

Ecosystem Diversity Definition

Variations in plant and animal species living together in a specific region, differing between locations

Bioprospecting Definition & Focus

Science-driven, exploratory search for biological resources for broad commercial or industrial innovation without necessarily relying on traditional knowledge

Ethnopharmacology Definition & Focus

Culture-driven study of traditional medicinal practices to preserve, understand, and validate traditional knowledge

Bioprospecting

Bioprospecting utilizes High-Throughput Screening (HTS)

Ethnopharmacology

Ethnopharmacology utilizes Low-Throughput Screening

True Ethnopharmacological Approach Key Tasks

1) Study pharmacological effects of most used species,
2) Develop local ethnopharmacopeias
3) Characterize relevant constituents
4) Formulate improved, simple galenical preparations

Top-Down Approaches Definition

Traditional natural product discovery starting from biomass without requiring gene sequencing; best for reproducibly abundant compounds

4 Major Elements of Top-Down Approaches

1) Biomass Acquisition
2) Effective Screening
3) Bioassay-directed Fractionation
4) Rapid and Effective Structure Elucidation

Typical Screening Pass Criteria Example

Extracts inhibiting microbial growth by 80% or more pass and proceed to isolation, structure elucidation, and lead identification

Golden Rule of Purification Steps

Tested for bioactivity at every step of purification to ensure activity is not lost

Diverse Sampling and Culturing Purpose

Explores diverse organisms and culture conditions (e.g., soil fungi) to indirectly optimize plant growth and secondary metabolite production

Bioassay-guided

Bioassay-guided isolates a single, highly potent compound

Synergy-directed

Synergy-directed assesses whether multiple components act synergistically

Major Limitations of Fractionation

Bias toward easily isolated compounds, active compounds represent a subset of the crude extract, and inability to isolate/test all compounds

Untargeted Metabolomics Definition & Techniques

Unbiased broad analysis of all metabolites in a sample via LC-MS to create chemical fingerprints without initial bioactivity data

Biochemometrics

Application of statistical methods to correlate chemical profiles (MS data) directly with biological activity

Biochemometrics Statistical Plots

Partial Least Square (PLS: Scores & Loadings Plots), Orthogonal Partial Least Square Discriminatory Analysis (OPLS-DA: S-Plot), and Selectivity Ratio Analysis

High-Throughput Screening (HTS) Model Organisms

Cell cultures or small non-human models such as fruit flies, frogs, and zebrafish (chosen for transparency)

Bottom-Up Approaches Definition

Starting with a known target, compound, gene, or biosynthetic pathway and moving toward natural product production

SMURF (Secondary Metabolite Unknown Regions Finder)

Bioinformatic tool that predicts backbone genes in fungal genomes for nonribosomal peptides, polyketides, indole alkaloids, and terpenes

antiSMASH

Antibiotics and Secondary Metabolite Analysis Shell that expands coverage across whole genome ranges of biosynthetic loci

Native Host Expression Strategies

Gene Knockout & Comparative Metabolomics, Kinase Knockout, and "Knock-in" Promoter Replacement Strategy

"Knock-In" Promoter Replacement Function

Activates silent natural product gene clusters by replacing native promoters with active ones (e.g., in Aspergillus nidulans)

Heterologous Host Expression Definition

Expressing a gene cluster in a different, genetically tractable host organism (e.g., E. coli or Streptomyces griseus)

Heterologous Expression Advantages

Highly efficient, faster, enables combinatorial biosynthesis, and faces fewer ethical restrictions